This question is being asked here quite frequently. The last time just a few days ago so it is worthwhile to look through the mailing list archive. But this is also answered in the FAQ (
http://ambermd.org/questions.html). So probably best to read through those valuable resources and come back with specific questions if necessary.
In short: there is no preset "recipe" except for you to understand what you are actually trying to achieve.
________________________________________
From: Bin ZOU [zoubin1025.gmail.com]
Sent: 18 March 2016 05:51
To: amber.ambermd.org
Subject: [AMBER] The basis for selecting step sizes
Hi everyone,
I just carried out a series of simulation steps, including an energy
minimization for 1000 steps, a heating for 50ps from 0k to 300k, a density
equilibration for 50ps, a constant-pressure equilibration for 500ps, and a
production MD for 2ns. Before this, I also added a 10 angstrom buffer of
water around the system in addition to the already defined crystallographic
waters.
The question is that if there is any basis for selecting these step sizes
(1000 steps, 50ps, etc.) and boundary condition artifacts?
Another question is for the time to do the production MD. It is said that,
in such short time simulation (2ns), most of the structures we observed are
very similar to the starting structure. As I started the simulation from a
relative stable structure (Crystal structure by X-ray diffraction), how
long should I perform the simulation? Is there any benchmark?
Thanks very much.
--
Regards,
ZOU, Bin
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Received on Fri Mar 18 2016 - 00:30:03 PDT
